[firedrake] Firedrake Installation
Andrew McRae
a.mcrae12 at imperial.ac.uk
Sun Nov 16 14:39:35 GMT 2014
On 16 November 2014 14:22, Rathgeber, Florian <
florian.rathgeber at imperial.ac.uk> wrote:
> [Please keep list in CC]
>
> On 16/11/14 14:12, Lee, Suet wrote:
> > Not sure if I'm doing it correctly but I tried this:
> >
> > mosh at ubuntu:~$ dpkg -s mpich2
> > dpkg-query: package 'mpich2' is not installed and no information is
> > available
> > Use dpkg --info (= dpkg-deb --info) to examine archive files,
> > and dpkg --contents (= dpkg-deb --contents) to list their contents.
> >
> > So the problem isn't down to mpich2?
>
> Sorry, the package you want to look for is libmpich-dev
>
> Is there any reason to use a 32bit system? We explicitly do *not*
> support 32bit systems and there isn't really a reason not to use 64bit.
>
Ah, I wasn't aware of this.
Context: Suet got the following error when she tried powering up a 64bit
VM, a couple of months ago:
"This virtual machine is configured for 64-bit guest operating systems.
However, 64-bit operation is not possible.
This host does not support Intel VT-x.
For more detailed information, see http://vmware.com/info?id=152."
[The graphics problem was something different]
I guessed that pointing her at the 32bit Ubuntu iso would be easier than
making BIOS changes (assuming her processor does support VT-x, but that
it's disabled in BIOS).
Florian: do you think the problem is related to 32bit-ness? If so, Suet
can bring her laptop to Huxley or WPL some time this week and we'll go the
64bit route.
Andrew
Florian
>
> > Suet
> >
> >
> > ------------------------------------------------------------------------
> > *From:* Andrew McRae <a.mcrae12 at imperial.ac.uk>
> > *Sent:* 16 November 2014 13:41
> > *To:* Lee, Suet
> > *Subject:* Re: Firedrake Installation
> >
> > I have no idea, but I've forwarded your problem to the Firedrake mailing
> > list; some people on there know a lot more than me about MPI.
> >
> > On 16 November 2014 13:28, Lee, Suet <suet.lee11 at imperial.ac.uk
> > <mailto:suet.lee11 at imperial.ac.uk>> wrote:
> >
> > I ran the install mpi4py commange but I have a new error now:
> >
> >
> > mosh at ubuntu:~$ wget -O -
> > https://github.com/OP2/PyOP2/raw/master/install.sh | sudo bash
> > --2014-11-16 13:20:14--
> > https://github.com/OP2/PyOP2/raw/master/install.sh
> > Resolving github.com <http://github.com> (github.com
> > <http://github.com>)... 192.30.252.131
> > Connecting to github.com <http://github.com> (github.com
> > <http://github.com>)|192.30.252.131|:443... connected.
> > HTTP request sent, awaiting response... 302 Found
> > Location:
> > https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh
> > [following]
> > --2014-11-16 13:20:16--
> > https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh
> > Resolving raw.githubusercontent.com
> > <http://raw.githubusercontent.com> (raw.githubusercontent.com
> > <http://raw.githubusercontent.com>)... 185.31.18.133
> > Connecting to raw.githubusercontent.com
> > <http://raw.githubusercontent.com> (raw.githubusercontent.com
> > <http://raw.githubusercontent.com>)|185.31.18.133|:443... connected.
> > HTTP request sent, awaiting response... 200 OK
> > Length: 3667 (3.6K) [text/plain]
> > Saving to: ‘STDOUT’
> >
> > 100%[======================================>] 3,667 --.-K/s
> > in 0s
> >
> > 2014-11-16 13:20:16 (40.6 MB/s) - written to stdout [3667/3667]
> >
> > PyOP2 installation started at Sun Nov 16 13:20:16 GMT 2014
> > on Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10
> > 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux
> >
> > *** Privileged installation ***
> > Running unprivileged commands as mosh
> >
> > *** Preparing system ***
> >
> > *** Installing dependencies ***
> >
> > *** Installing PETSc ***
> >
> > *** Installing PyOP2 ***
> >
> > [ubuntu:31603] *** Process received signal ***
> > [ubuntu:31603] Signal: Floating point exception (8)
> > [ubuntu:31603] Signal code: Integer divide-by-zero (1)
> > [ubuntu:31603] Failing at address: 0xb74d6da0
> > [ubuntu:31603] [ 0] [0xb779a40c]
> > [ubuntu:31603] [ 1] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2cda0)
> > [0xb74d6da0]
> > [ubuntu:31603] [ 2] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2e71c)
> > [0xb74d871c]
> > [ubuntu:31603] [ 3] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2ea8b)
> > [0xb74d8a8b]
> > [ubuntu:31603] [ 4] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x98f6)
> > [0xb74b38f6]
> > [ubuntu:31603] [ 5]
> > /usr/lib/i386-linux-gnu/libhwloc.so.5(hwloc_topology_load+0x1c6)
> > [0xb74b48ec]
> > [ubuntu:31603] [ 6]
> > /usr/lib/libopen-rte.so.4(orte_odls_base_open+0x7b1) [0xb76fa881]
> > [ubuntu:31603] [ 7]
> > /usr/lib/openmpi/lib/openmpi/mca_ess_hnp.so(+0x2445) [0xb7488445]
> > [ubuntu:31603] [ 8] /usr/lib/libopen-rte.so.4(orte_init+0x1cf)
> > [0xb76cfb3f]
> > [ubuntu:31603] [ 9] /usr/lib/libopen-rte.so.4(orte_daemon+0x256)
> > [0xb76ec1c6]
> > [ubuntu:31603] [10] orted() [0x80485b3]
> > [ubuntu:31603] [11]
> > /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0xb7504a83]
> > [ubuntu:31603] [12] orted() [0x80485f8]
> > [ubuntu:31603] *** End of error message ***
> > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a
> > daemon on the local node in file ess_singleton_module.c at line 343
> > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a
> > daemon on the local node in file ess_singleton_module.c at line 140
> > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a
> > daemon on the local node in file runtime/orte_init.c at line 128
> >
> --------------------------------------------------------------------------
> > It looks like orte_init failed for some reason; your parallel
> process is
> > likely to abort. There are many reasons that a parallel process can
> > fail during orte_init; some of which are due to configuration or
> > environment problems. This failure appears to be an internal
> failure;
> > here's some additional information (which may only be relevant to an
> > Open MPI developer):
> >
> > orte_ess_set_name failed
> > --> Returned value Unable to start a daemon on the local node
> > (-128) instead of ORTE_SUCCESS
> >
> --------------------------------------------------------------------------
> >
> --------------------------------------------------------------------------
> > It looks like MPI_INIT failed for some reason; your parallel process
> is
> > likely to abort. There are many reasons that a parallel process can
> > fail during MPI_INIT; some of which are due to configuration or
> > environment
> > problems. This failure appears to be an internal failure; here's
> some
> > additional information (which may only be relevant to an Open MPI
> > developer):
> >
> > ompi_mpi_init: orte_init failed
> > --> Returned "Unable to start a daemon on the local node" (-128)
> > instead of "Success" (0)
> >
> --------------------------------------------------------------------------
> > [ubuntu:31601] *** An error occurred in MPI_Init_thread
> > [ubuntu:31601] *** on a NULL communicator
> > [ubuntu:31601] *** Unknown error
> > [ubuntu:31601] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
> >
> --------------------------------------------------------------------------
> > An MPI process is aborting at a time when it cannot guarantee that
> all
> > of its peer processes in the job will be killed properly. You should
> > double check that everything has shut down cleanly.
> >
> > Reason: Before MPI_INIT completed
> > Local host: ubuntu
> > PID: 31601
> >
> --------------------------------------------------------------------------
> > PyOP2 installation failed
> > See /home/mosh/PyOP2/pyop2_install.log for details
> >
> > Any idea what's going on?
> >
> > Suet
> >
> >
> >
> ------------------------------------------------------------------------
> > *From:* Andrew McRae <a.mcrae12 at imperial.ac.uk
> > <mailto:a.mcrae12 at imperial.ac.uk>>
> > *Sent:* 15 November 2014 23:13
> > *To:* Lee, Suet
> > *Subject:* Re: Firedrake Installation
> >
> > Or, if you want to be a guinea pig, don't run the 'sudo pip install
> > mpi4py' command and just run the install script again :)
> >
> > (I updated
> > <
> https://github.com/OP2/PyOP2/commit/e15b3ee8d72369f10c9a84d944a3ecbf06f7e927
> >
> > the script just now -- thanks for alerting us to that bug)
> >
> > On 15 November 2014 23:09, Andrew McRae <a.mcrae12 at imperial.ac.uk
> > <mailto:a.mcrae12 at imperial.ac.uk>> wrote:
> >
> > Hi Suet,
> >
> > Sorry about that. This should fix the mpi4py problem: sudo pip
> > install mpi4py
> >
> > Then try the quick install script again.
> >
> > Yes, PyOP2, FFC, FIAT and UFL need to be installed before
> > firerake. However, installing FFC/FIAT/UFL is easy -- you just
> > run the 'sudo pip install \ six \ sympy \ ...' command, as
> > described on http://www.firedrakeproject.org/download.html.
> >
> > Let me know if there's any other problems.
> >
> > Best,
> >
> > Andrew
> >
> >
> > On 15 November 2014 23:00, Lee, Suet <suet.lee11 at imperial.ac.uk
> > <mailto:suet.lee11 at imperial.ac.uk>> wrote:
> >
> > Hi Andrew,
> >
> >
> > So I finally got round to the Firedrake installation!
> >
> >
> > I'm trying to install PyOP2. The only problem is that I'm
> > running up against the following error:
> >
> >
> > PyOP2 installation started at Sat Nov 15 22:38:45 GMT 2014
> > on Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr
> > 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux
> >
> > *** Privileged installation ***
> > Running unprivileged commands as mosh
> >
> > *** Preparing system ***
> >
> > *** Installing dependencies ***
> >
> > *** Installing PETSc ***
> >
> > *** Installing PyOP2 ***
> >
> > Traceback (most recent call last):
> > File "<string>", line 1, in <module>
> > File "pyop2/__init__.py", line 9, in <module>
> > from op2 import *
> > File "pyop2/op2.py", line 38, in <module>
> > import backends
> > File "pyop2/backends.py", line 41, in <module>
> > from logger import warning
> > File "pyop2/logger.py", line 38, in <module>
> > from mpi import MPI
> > File "pyop2/mpi.py", line 37, in <module>
> > from mpi4py import MPI as _MPI
> > ImportError: No module named mpi4py
> > PyOP2 installation failed
> > See /home/mosh/pyop2_install.log for details
> >
> >
> > I must be missing the file mpi4py? Do I have to install
> >
> > PyOP2 <http://op2.github.io/PyOP2>, FFC
> > <https://bitbucket.org/mapdes/ffc>, FIAT
> > <https://bitbucket.org/mapdes/fiat>, and UFL
> > <https://bitbucket.org/mapdes/ufl>, before Firedrake? I
> > attempted the quick installation for PyOP2 but do I need to
> > install other packages before that?
> >
> > Best,
> >
> > Suet
>
>
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